Those were hard, 5 matches in a row and Espeon basically destroys half your team if you aren't super prepared for it. Totally agree with all the other trainers people are posting. Though there is one guy in BW with a Bouncing Mantine that gave my friends a lot of trouble...

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Umbreon was difficult as well, it stalled my team and wears them down for the rest. Stall doesn't work as the player, but it's very annoying to have to fight, especially with following battles.

Yes, I know I never post in this sub-forum, but wth, I've been a fan of the games so I might as well.

I'd just like to give a special SCREW YOU to the first Gorigan fight in Pokemon XD. That fight alone forced me to use Pidgeot on my XD team. I mean, seriously, a pre-ending DEDICATED Protect+EQ team!? In addition, there weren't a whole lot of Pokemon immune to Earthquake you could use in XD to my recollection. Even though none of his mons get STAB, the Earthquakes still hit pretty hard.

But that's not all. At the same time, I was trying to capture his Primeape and Hypno while all this crap was happening, and, btw neither of the two have Protect so they can die rather quickly and they have powerful Shadow moves you have to be wary of. It was hell for me to get through this fight as a kid. I think I played it at least 15 times before I won, and it was after my Arbok had finished spamming Shadow Half and was down to only 3 HP, not to mention it was the only Pokemon still alive. So yeah, that battle was hard as hell.

Specifically the final set. It's a 6 in a row battle against increasingly tough trainers and must be done all in a row with no chance to heal between battles.
It's kind of ridiculous and I'm a little sad you can only do it once (unless you lose, obviously)

Yes, I know I never post in this sub-forum, but wth, I've been a fan of the games so I might as well.

I'd just like to give a special SCREW YOU to the first Gorigan fight in Pokemon XD. That fight alone forced me to use Pidgeot on my XD team. I mean, seriously, a pre-ending DEDICATED Protect+EQ team!? In addition, there weren't a whole lot of Pokemon immune to Earthquake you could use in XD to my recollection. Even though none of his mons get STAB, the Earthquakes still hit pretty hard.

But that's not all. At the same time, I was trying to capture his Primeape and Hypno while all this crap was happening, and, btw neither of the two have Protect so they can die rather quickly and they have powerful Shadow moves you have to be wary of. It was hell for me to get through this fight as a kid. I think I played it at least 15 times before I won, and it was after my Arbok had finished spamming Shadow Half and was down to only 3 HP, not to mention it was the only Pokemon still alive. So yeah, that battle was hard as hell.

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Cipher Admin Dakim also runs an EQ+Protect team in Pokemon Colleseum. His shadow Pokemon, Entei, does not have Protect. Also, Entei has a very low capture rate in Collesseum, so it is difficult to capture, especially since Shadow Rush does recoil damage.

But then again he does use a Metang.

Then there is Cipher Admin Venus, Attract team that also spreads other status around. So frustrating.

Cipher Admin Ein has a Rain Dance/Thunder team.

Then there is Evice, who has his Slowking use Skill Swap on his Slaking, which proceeds to go on a rampage with Earthquake.

Also the Ciper Admin AIs in Colosseum were total cheaters. If you have one Pokemon left in the double battle, and use its turn to revive another Pokemon, they can target the one you revived on the turn it switches in. Dakim is probably the hardest (at least the rematch, I don't think the first fight was that bad as long as you could catch Entei) because there's really nothing that you could have that will be able to take Earthquakes, sun-boosted Fire Blasts, and Solarbeams (Edit: Mantine might do ok, but it's not much of a threat under sun). Venus just uses a bunch of hax, and I never had trouble with her except once when I couldn't kill her ingrain+leech seed+giga drain meganium in the rain. Ein gets owned by grass types, a lot of which conveniently get sunny day. Evice can be really threatening, but his AI seems to not pull of the skill swap very often (even if he does, Slaking can't touch Skarmory or Misdreavus at all).

Oh i almost forgot, In HG Lance. I mean my team was composed of a Lv. 49 Ho-Oh, Lv. 50 Typhlosion, Lv.42 Gyarados, Lv.45 Rydon, Lv.37 Dragonair, Lv.43 Ampharos, and a Lv.43 Mamoswine and no meds. He screwed my Typhlosion with Gyarados, and also Ho-Oh with Aerodactyl. He then Sends out Dragonite #1 with thunder and i send out Rhydon who faints it with 2 stone edge . He then Sends out Dragonite #2 with blizzard same drill, sends out Gyarados and i use stone edge once again but he uses Waterfall OHKO Rhydon. I send out Ampharos, Gyarados (thank god) used Dragon Pulse while i OHKO him with Discharge. He Sends out Charizard who uses Air Slash while i Use Thunder OHKOing it. Finally he Sends out Dragonite No. 3 who uses Outrage while use Thunder Wave. Again he uses Outrage and KOs Ampharos. I send out Mamoswine who uses Ice Fang and OHKO's Dragonite. Finally i beat Lance all with the help of my fine pokemon and some help from some Inspirational Music i.e Don't Stop Believing

I already knew and suffered through series classic like Misty's Starmie and Whitney's Miltank, but my memory is not all that it was and this thread reminded me of so much stuff I went through!
The Rocket's Raticate, that Cool Trainer's Milotic, Winona's Earthquaking Altaria, Platinum's Fantina and her Mismagius... good times.

I remember a difficult match in Emerald that no one mentioned: Tate & Lisa.
After the joke that they were in RS, I went in unprepared and got thoroughly demolished.
I remember suffering through Steven's steel team in RS. "What the hell is a Metagross?!"
That's the fight that taught me the amazing death-fodder HM slave + revive strategy lol

Some of the recent ones in BW are also instant "classics":
-Elesa's Volt Switching antics and her Ground-immune electrics
-Ghetsis' Hydreigon. That thing was just not fair. Sacrificial Patrat FTW (hahaha I also remember my friend's sacrificial Lilipup. Took a Crit from Shantaul's Chandelure for the team!)

I played through a Japanese copy of BW2, here are some that game me a lot of trouble:
[WARNING: probably some SPOILERS ahead]

-The first gym leader.
I lost that fight like 7 times. I'm wish I was kidding. And this is from a guy who's played almost everything since RB. People say use Riolu's Counter but that doesn't really work when Riolu get's OHKOed. That damn Lilipup just DESTROYS everything.
Wanna know what I did? Thunderwave + Growl spam Mareep. Talk about forcing you to use a strategy! XD

-The Colress battle on the ship.
He has 5 steel types I believe. I had a Lucario and an Emboar, not to mention the rest of my kick ass team. They all got they ass kicked instead. I honestly don't know what happened, my team members were falling like flies.
I won the fight with a single Pokemon left. He was at half HP and paralyzed; incredibly close battle.

-The last difficult battle I had was against Caitlin.
Her Pokemon would never faint to a single attack, and her Yawn-spamming Musharna guaranteed one of my Pokemon out cold. The rest of the battle was incredibly tough, the toughest out of the E4+Champion (for me at least).

Sabrina in original Red/Blue/Yellow. Considering how overpowered Psychic types were in those days, it's a wonder anyone can beat her without just outleveling her.

Also Clair and Lance in HGSS. Clair's Kingdra is just...overpowered considering how few effective counters exist for Kingdra at that point in the game. Lance his army of Dragonites are just plain annoying the first time around, but when you battle him in a rematch you can kiss some Pokemon goodbye. The tag battle against these two is also not all that pleasant.

-The last difficult battle I had was against Caitlin.
Her Pokemon would never faint to a single attack, and her Yawn-spamming Musharna guaranteed one of my Pokemon out cold. The rest of the battle was incredibly tough, the toughest out of the E4+Champion (for me at least).

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I didn't have any trouble with Caitlin, but only because I was using Zoroark. I just put a Pokemon that I knew she'd use Psychic attacks against last in my party and never took any damage. Manipulating AI FTW.

Once, during a crystal nuzlocke, I was about to finish it with the fight against Red and DID NOT feel like grinding.. So I just stocked on the X items and set up my fairly freshly caught Belly Drum Snorlax against Pikachu. iirc I 6-0'd him, either that or a 5-0. :D And so I took down the undoubtedly strongest trainer in Kanto without the death of any pokemon.. Red. B-)

Those were hard, 5 matches in a row and Espeon basically destroys half your team if you aren't super prepared for it. Totally agree with all the other trainers people are posting. Though there is one guy in BW with a Bouncing Mantine that gave my friends a lot of trouble...

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Remember my Soul Silver Scramble from Mk I? Those kimono girls were really tough! After Umbreon and Espeon went down, all I had left was Beatdown the Lanturn. But she was a hard counter to Flareon, Jolteon (thank you Volt Absorb Ability!), and Vaporeon.

Colosseum in general was the most difficult (relative) Pokemon RPG in my opinion. The traditional grinding for experience route wasn't really applicable since you don't have the nice and slow lv2 Pidgeys to practice on and everything is usually around your level or above. You have a limited selection of Pokemon to use with limited movepools and you can't use them to their fullest potential right away because all you have is Shadow Rush and usually useless moves until close to purification. Besides my first original Red runthrough which I had trouble with because I was six years old, Colosseum is the only other Pokemon game I had trouble clearing the first time through. I really loved the game and how challenging (relative) it was, B2 challenge mode can't compare. I have to emphasize it wasn't that hard, but it was for a Pokemon game.

On topic: point is that all of the bosses in Colosseum were difficult relative to the other Pokemon games. Especially Dakim, Venus, and Ein who would just kill you while you fail to catch their legendaries with a catch rate of 2 with an underleveled Noctowl as your only sleep move...

I am not sure what it is about Normal Gym Leaders but they are a royal pain. First Whitney and that damn bovine, then Norman (I got lucky with Breloom learning Mach Punch and Counter), and then Lenora and Cheren. For a first gym leader, Cheren was hard. Using some sacrificing and Azurill with Frustration I some how won.

I rotated 12 mons for my B/W team, so Ghetsis was a complete bitch. I finally got a Boldore and taughtit Toxic to beat Hydreigon. Sturdy is great. HGSS Lance was pretty easy for me, but then again I was using Ice Beam Porygon2 and the Steelix I evolved from the Onix in-game trade.

EDIT: Emerald Wattson really was hard too. I picked Treecko, and had to resort to using SHEDINJA to beat him.

The worst battles i've ever had were in platinum, especially the double battles with my rival. The one before the battle frontier is terrible;he contributes very little, so it's basically like a 2v1 every time. Once his pokemon go down... have fun!!

Not to mention the first one, in which he leads off with a MUNCHLAX. So it won't die and it won't do anything useful but try not to die!

misty in fire red. shes upgraded to water pulse which has insane confusion hax. even a pikachu 5 levels higher struggles against that starmie.

ghetsis is pretty easy except for that blasted hydreigon. it OHKOs everythingin one shot and was faster than my reshiram. i beat him with stoutland but i lost a couple of times before that. i had to teach it giga impact to kill it which nobody should ever have to do.

misty in fire red. shes upgraded to water pulse which has insane confusion hax. even a pikachu 5 levels higher struggles against that starmie.

ghetsis is pretty easy except for that blasted hydreigon. it OHKOs everythingin one shot and was faster than my reshiram. i beat him with stoutland but i lost a couple of times before that. i had to teach it giga impact to kill it which nobody should ever have to do.

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I beat Misty's Starmie with my Beedrill, only one or two levels higher than it. I outsped and OHKO'd with Twineedle. (although one of the hits may have been a crit). Just saying.

I lost to misty 5 times in row when i was playing red for the first time. The 1st battle with blue west of virhdian was also tough. Oh and that rocket grunt in mt. moon with raticate. But the toughest battle for me was the battle with sabrina. Whitney's miltank was a big challenge in gs. But i had most difficulty against clair. I had only 1 electric type attacker-kadabra. When i switch him gyardos used hyper beam. This was the 1st ever battle when i used a death fooder.

One word.
Colress. You sneaky bastard.
Making me forget you had a monotype steel. Gahh.
Maybe Iris' Aggron, if that thing sets up, GAME FUCKING OVER.
Maybe Tucker from the Battle Dome.
Maybe Veteran Sinan and Veteran Rosaline in Pinwheel Forest BW2. My team was barely lvl 60 when I got there.